The aerodynamic characteristics of advanced low-pressure turbines could be affected by the interaction between the transitional and turbulent flow and the dynamic behaviour of the blades. Consequently, analysing the details of the interactions between the transient flow, blades vibrations, and the flutter occurrence over the blades in LPTs, are essential in order to enhance the aerodynamic efficiency of the modern LPT turbines. The distinctive feature of the present analysis is performing high-fidelity simulations based on a DNS approach employing a 3D blade model to investigate the flutter instabilities in a T106A turbine at various inter blade phase angles (IBPAs) at different Reynolds numbers. The impacts of the flutter on the transient flow structure are examined by using a direct numerical simulation method. The results show that at IBPA=0∘, persistent patterns of vortex generation are detected with fluid flow mixing in the downward areas. For IBPA=180∘, however, the recirculation generated by the upper blades proceeds toward the lower ones and interfere with the shedding from the trailing edge which impact the wake structure in the downstream regions significantly. A three-dimensional frequency domain model based on the harmonic balance method is also proposed in this study to investigate the capabilities and limitations of frequency domain methods in predicting aeroelasticity and details of flow structures in LPTs.